CDSSet {IsoformSwitchAnalyzeR} | R Documentation

## Container for coding sequence (CDS) annotation information

### Description

A container for coding sequence annotation information.

### Usage

    CDSSet(cds)

### Arguments

`cds` | A `data.frame` object containing CDS annotation. See details for required columns.

### Details

This object can be generated automatically from `getCDS`, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:

`chrom`, the chromosome name (NB: chromosome names must match when running `analyzeORF`). `strand`, the strand, `cdsStart`, the genomic start of the coding sequence (beware of 0/1-frame issues), and `cdsEnd`, the genomic end of the coding sequence (beware of 0/1-frame issues).

The `CDSset` object is used with `analyzeORF` if annotated TSS should be analyzed.

For an example, see `getCDS`.

### Value

A `CDSSet` object.

### Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

### References

Vitting-Seerup K, et al: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014, 15:81.

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]